I dont know if it is a common issue but the 'Retro' Shader Mode with 'Pixel Perfect' set to OFF does not work perfectly with SEGA CD games, everything else works perfectly fine even in 1080p display resolution, I mean there are no display artifacts and the picture looks amazing even when viewing it in 1080p on a 720p native projector. The scanlines line up perfectly on other console games but not in SEGA CD games!, please see screenshots below:
SEGA MEGA DRIVE:
See highlighted below:
I dont know what setting to set RetroArch to fix the same.